def test_negative_residue_numbers_2jaj():
mol = mdt.read(get_data_path('2jaj.pdb'))
res = mol.chains['B'].residues[0]
assert res.pdbindex == -4
assert res.index == 272
assert res.name == 'GLY-4'
mread = mdt.read(mol.write('pdb'),
format='pdb')
res = mread.chains['B'].residues[0]
assert res.pdbindex == -4
assert res.index == 272
assert res.name == 'GLY-4'
def test_frame_to_molecule_conversion(precanned_trajectory):
traj = precanned_trajectory
f0_position = u.angstrom*[[1, 0, 0],
[0, 0, 0],
[0, 1, 0]]
f2_position = u.angstrom*[[2, 0, 0],
[-1, 0, 0],
[-1, 1, 0]]
f0 = traj.frames[0]
mol = f0.as_molecule()
assert mol.same_topology(traj.mol)
assert (mol.positions == f0_position).all()
assert mol.time == 0.0 * u.fs
# test ability to directly write a frame
readmol = mdt.read(f0.write('xyz'), format='xyz')
np.testing.assert_allclose(readmol.positions.value_in(u.angstrom),
f0_position.value_in(u.angstrom))
m2 = traj.frames[-1].as_molecule()
assert m2.same_topology(mol)
assert (m2.positions == f2_position).all()
assert m2.time == 2.0 * u.fs
def test_disulfide_bond_detection_1hpk():
mol = mdt.read(get_data_path('1hpk.pdb'))
mol = mdt.interfaces.ambertools._prep_for_tleap(mol)
for residx in (0, 21, 49, 61, 73, 78):
residue = mol.residues[residx]
assert residue.resname == 'CYX'
assert residue.name[:3] == 'CYX'
def test_missing_terminal_atoms_3ac2():
""" Tests that we can still detect terminal residues even if the peptide-bonded atoms
are missing from the structure
"""
mol = mdt.read(get_data_path('3ac2.pdb'))
assert mol.chains['A'].n_terminal is not None
assert mol.chains['A'].c_terminal is not None
def mol_from_sdf():
return mdt.read("""
OpenBabel02271712493D
11 10 0 0 0 0 0 0 0 0999 V2000
0.9114 -0.0615 0.0032 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4168 1.3750 0.0264 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9114 2.1503 -1.1831 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5568 -0.5828 -0.8916 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5460 -0.6043 0.8807 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0053 -0.0987 0.0111 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6785 1.3847 0.0446 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7625 1.8663 0.9425 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5568 1.6932 -2.1123 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5460 3.1815 -1.1499 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0053 2.1774 -1.2097 H 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 2 1 0 0 0 0
4 1 1 0 0 0 0
5 1 1 0 0 0 0
6 1 1 0 0 0 0
7 2 1 0 0 0 0
8 2 1 0 0 0 0
9 3 1 0 0 0 0
10 3 1 0 0 0 0
11 3 1 0 0 0 0
M END
$$$$
""",
format='sdf')
def cached_mol_from_sdf():
return mdt.read("""
OpenBabel02271712493D
11 10 0 0 0 0 0 0 0 0999 V2000
0.9114 -0.0615 0.0032 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4168 1.3750 0.0264 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9114 2.1503 -1.1831 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5568 -0.5828 -0.8916 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5460 -0.6043 0.8807 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0053 -0.0987 0.0111 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6785 1.3847 0.0446 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7625 1.8663 0.9425 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5568 1.6932 -2.1123 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5460 3.1815 -1.1499 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0053 2.1774 -1.2097 H 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 2 1 0 0 0 0
4 1 1 0 0 0 0
5 1 1 0 0 0 0
6 1 1 0 0 0 0
7 2 1 0 0 0 0
8 2 1 0 0 0 0
9 3 1 0 0 0 0
10 3 1 0 0 0 0
11 3 1 0 0 0 0
M END
$$$$
""", format='sdf')
def test_compressed_write(bipyridine_xyz, tmpdir, suffix):
# Note: compressed read is tested elsewhere when reading test data files
path = pathlib.Path(native_str(tmpdir))
dest = path / ('bipyr.xyz.' + suffix)
bipyridine_xyz.write(dest)
# don't use MDT's reader here! Need to make sure it's really gzip'd
if suffix == 'gz':
opener = gzip.open
elif suffix == 'bz2':
opener = bz2.BZ2File
else:
raise ValueError('Unrecognized suffix "%s"' % suffix)
if PY2:
mode = 'r'
else:
mode = 'rt'
if suffix == 'bz2':
opener = bz2.open
with opener(str(dest), mode) as infile:
content = infile.read()
mol = mdt.read(content, format='xyz')
assert mol.num_atoms == bipyridine_xyz.num_atoms
def test_compressed_write(bipyridine_xyz, tmpdir, suffix):
# Note: compressed read is tested elsewhere when reading test data files
path = pathlib.Path(native_str(tmpdir))
dest = path / ('bipyr.xyz.' + suffix)
bipyridine_xyz.write(dest)
# don't use MDT's reader here! Need to make sure it's really gzip'd
if suffix == 'gz':
opener = gzip.open
elif suffix == 'bz2':
opener = bz2.BZ2File
else:
raise ValueError('Unrecognized suffix "%s"' % suffix)
if PY2:
mode = 'r'
else:
mode = 'rt'
if suffix == 'bz2':
opener = bz2.open
with opener(str(dest), mode) as infile:
content = infile.read()
mol = mdt.read(content, format='xyz')
assert mol.num_atoms == bipyridine_xyz.num_atoms
def test_missing_residues_xtal_2jaj():
mol = mdt.read(get_data_path('2jaj.pdb'))
missingres = mol.metadata.missing_residues
for expected in MISSINGRES_2JAJ:
assert missingres[expected[0]][expected[2]] == expected[1]
def test_write_file_to_buffer(bipyridine_smiles):
mol = bipyridine_smiles
buffer = native_str_buffer()
mol.write(buffer, format='pdb')
buffer.seek(0)
newmol = mdt.read(buffer.getvalue(), format='pdb')
assert mol.num_atoms == newmol.num_atoms
def test_write_file_to_buffer(bipyridine_smiles):
mol = bipyridine_smiles
buffer = native_str_buffer()
mol.write(buffer, format='pdb')
buffer.seek(0)
newmol = mdt.read(buffer.getvalue(), format='pdb')
assert mol.num_atoms == newmol.num_atoms
def test_amber_tleap():
mol = mdt.read('../data/nuc.pdb')
model = moldesign.methods.models.OpenMMPotential(implicit_solvent='obc',
cutoff=8.0 * u.angstrom,
force_field='ff14SB')
mol.set_energy_model(model)
result = mol.calculate(wait=True)
assert 'potential_energy' in result and 'forces' in result
def test_topology_preserved_in_serialization(bipyridine_smiles, fmt):
""" Test that bond topology is preserved even if it doesn't make sense from distances
"""
mol = bipyridine_smiles.copy() # don't screw up the fixture object
mol.bond_graph[mol.atoms[3]][mol.atoms[5]] = 3
mol.bond_graph[mol.atoms[5]][mol.atoms[3]] = 3
mol.atoms[3].x += 10.0 * u.angstrom
newmol = mdt.read(mol.write(format=fmt), format=fmt)
assert mol.same_bonds(newmol, verbose=True)
def test_topology_preserved_in_serialization(bipyridine_smiles, fmt):
""" Test that bond topology is preserved even if it doesn't make sense from distances
"""
if fmt != 'pkl':
pytest.xfail("We are currently unable to get an unambiguous representation of a molecular "
"sructure with ANY current file formats or parsers.")
mol = bipyridine_smiles.copy() # don't screw up the fixture object
mol.bond_graph[mol.atoms[3]][mol.atoms[5]] = 3
mol.bond_graph[mol.atoms[5]][mol.atoms[3]] = 3
mol.atoms[3].x += 10.0 * u.angstrom
newmol = mdt.read(mol.write(format=fmt), format=fmt)
assert mol.same_bonds(newmol, verbose=True)
def test_topology_preserved_in_serialization(bipyridine_smiles, fmt):
""" Test that bond topology is preserved even if it doesn't make sense from distances
"""
if fmt != 'pkl':
pytest.xfail(
"We are currently unable to get an unambiguous representation of a molecular "
"sructure with ANY current file formats or parsers.")
mol = bipyridine_smiles.copy() # don't screw up the fixture object
mol.bond_graph[mol.atoms[3]][mol.atoms[5]] = 3
mol.bond_graph[mol.atoms[5]][mol.atoms[3]] = 3
mol.atoms[3].x += 10.0 * u.angstrom
newmol = mdt.read(mol.write(format=fmt), format=fmt)
assert mol.same_bonds(newmol, verbose=True)
def test_numeric_residue_name_1PYN():
""" The ligand in this residue is named "941", which causes a little trickiness
"""
import parmed
mol = mdt.read(get_data_path('1pyn.pdb'))
ligand = mdt.Molecule(mol.residues[283])
params = mdt.parameterize(ligand, charges='gasteiger')
params.lib.put('/tmp/tmp.lib')
contents = parmed.load_file('/tmp/tmp.lib')
assert len(contents) == 1
assert contents.keys()[0] == '941'
def test_split_chains_3p3k():
mol = mdt.read(get_data_path('3p3k.pdb.gz'))
assert mol.num_chains == 1 # not really testing this, just for sanity's sake
newmol = mdt.split_chains(mol)
assert newmol.num_chains == 3
assert newmol.chains['A'] is newmol.chains[0]
assert newmol.chains['A'].type == 'protein'
assert newmol.chains['B'] is newmol.chains[1]
assert newmol.chains['B'].type == 'protein'
assert newmol.chains['C'] is newmol.chains[2]
assert newmol.chains['C'].type == 'water'
def test_split_chains_3p3k():
mol = mdt.read(get_data_path('3p3k.pdb'))
assert mol.num_chains == 1 # not really testing this, just for sanity's sake
newmol = mdt.split_chains(mol)
assert newmol.num_chains == 3
assert newmol.chains['A'] is newmol.chains[0]
assert newmol.chains['A'].type == 'protein'
assert newmol.chains['B'] is newmol.chains[1]
assert newmol.chains['B'].type == 'protein'
assert newmol.chains['C'] is newmol.chains[2]
assert newmol.chains['C'].type == 'water'
def mol_from_xyz():
return mdt.read("""43
c1.pdb
C -1.21700 1.04300 2.45300
C -0.14200 0.18700 2.19500
C -0.31600 -0.99500 1.46200
C -1.59800 -1.33100 1.02200
C -2.68200 -0.48500 1.28100
C -2.50400 0.70500 1.98200
O -3.53000 1.57400 2.25000
O -1.13200 2.21500 3.14700
C 0.14200 2.61500 3.63500
C 0.86700 -1.90600 1.12900
C 1.10600 -1.99700 -0.40500
O 2.06900 -1.52700 1.78600
O 1.81300 -0.81200 -0.83600
C 1.98100 -3.18300 -0.81100
O 2.18000 -3.27400 -2.21400
C 1.18300 0.32500 -1.28900
C 0.13100 0.33800 -2.23300
C -0.38800 1.56800 -2.65400
C 0.15900 2.77500 -2.20100
C 1.23000 2.75900 -1.31000
C 1.72800 1.53500 -0.85900
O -0.31100 -0.88000 -2.70600
C -1.43500 -0.90100 -3.58200
H 0.84400 0.42500 2.57000
H -1.77600 -2.25500 0.47700
H -3.67600 -0.75700 0.93200
H -4.35900 1.18400 1.93700
H -0.03000 3.54300 4.18500
H 0.84500 2.80900 2.81200
H 0.56300 1.86400 4.31600
H 0.63600 -2.91500 1.49500
H 0.14200 -2.06200 -0.91500
H 2.51900 -0.89500 1.20400
H 1.52900 -4.10700 -0.41600
H 2.97500 -3.07900 -0.36800
H 1.34400 -3.10100 -2.67400
H -1.20600 1.60000 -3.36300
H -0.25300 3.71600 -2.56000
H 1.68000 3.68900 -0.97300
H 2.55900 1.49100 -0.16100
H -1.60900 -1.95000 -3.81500
H -1.22800 -0.35800 -4.51600
H -2.32500 -0.48000 -3.09700
""",
format='xyz')
def cached_mol_from_xyz():
return mdt.read("""43
c1.pdb
C -1.21700 1.04300 2.45300
C -0.14200 0.18700 2.19500
C -0.31600 -0.99500 1.46200
C -1.59800 -1.33100 1.02200
C -2.68200 -0.48500 1.28100
C -2.50400 0.70500 1.98200
O -3.53000 1.57400 2.25000
O -1.13200 2.21500 3.14700
C 0.14200 2.61500 3.63500
C 0.86700 -1.90600 1.12900
C 1.10600 -1.99700 -0.40500
O 2.06900 -1.52700 1.78600
O 1.81300 -0.81200 -0.83600
C 1.98100 -3.18300 -0.81100
O 2.18000 -3.27400 -2.21400
C 1.18300 0.32500 -1.28900
C 0.13100 0.33800 -2.23300
C -0.38800 1.56800 -2.65400
C 0.15900 2.77500 -2.20100
C 1.23000 2.75900 -1.31000
C 1.72800 1.53500 -0.85900
O -0.31100 -0.88000 -2.70600
C -1.43500 -0.90100 -3.58200
H 0.84400 0.42500 2.57000
H -1.77600 -2.25500 0.47700
H -3.67600 -0.75700 0.93200
H -4.35900 1.18400 1.93700
H -0.03000 3.54300 4.18500
H 0.84500 2.80900 2.81200
H 0.56300 1.86400 4.31600
H 0.63600 -2.91500 1.49500
H 0.14200 -2.06200 -0.91500
H 2.51900 -0.89500 1.20400
H 1.52900 -4.10700 -0.41600
H 2.97500 -3.07900 -0.36800
H 1.34400 -3.10100 -2.67400
H -1.20600 1.60000 -3.36300
H -0.25300 3.71600 -2.56000
H 1.68000 3.68900 -0.97300
H 2.55900 1.49100 -0.16100
H -1.60900 -1.95000 -3.81500
H -1.22800 -0.35800 -4.51600
H -2.32500 -0.48000 -3.09700
""", format='xyz')
def test_frame_to_molecule_conversion(precanned_trajectory):
traj = precanned_trajectory
f0_position = u.angstrom * [[1, 0, 0], [0, 0, 0], [0, 1, 0]]
f2_position = u.angstrom * [[2, 0, 0], [-1, 0, 0], [-1, 1, 0]]
f0 = traj.frames[0]
mol = f0.as_molecule()
assert mol.same_topology(traj.mol)
assert (mol.positions == f0_position).all()
assert mol.time == 0.0 * u.fs
# test ability to directly write a frame
readmol = mdt.read(f0.write('xyz'), format='xyz')
np.testing.assert_allclose(readmol.positions.value_in(u.angstrom),
f0_position.value_in(u.angstrom))
m2 = traj.frames[-1].as_molecule()
assert m2.same_topology(mol)
assert (m2.positions == f2_position).all()
assert m2.time == 2.0 * u.fs
def pdb_3ac2():
return mdt.read(get_data_path('3ac2.pdb.bz2'))
def test_missing_atoms_3b5x():
mol = mdt.read(get_data_path('3b5x.cif.bz2'))
assert mol.num_chains == 2
assert mol.num_atoms == 1144
assert mol.num_residues == 1144
def bipyridine_sdf():
return mdt.read(get_data_path('bipyridine.sdf'))
def pdb_1pyn():
return mdt.read(get_data_path('1pyn.pdb.gz'))
def pdb_2jaj_roundtrip(pdb_2jaj):
return mdt.read(pdb_2jaj.write('pdb'), format='pdb')
def pdb_1hpk_roundtrip(pdb_1hpk):
return mdt.read(pdb_1hpk.write('pdb'), format='pdb')
def propane_pdb():
return mdt.read(get_data_path('propane.pdb'))
def pdb1yu8():
return mdt.read(get_data_path('1yu8.pdb'))
def bipyridine_mol2():
return mdt.read(get_data_path('bipyridine.mol2'))
def protein():
return mdt.read(helpers.get_data_path('3aid.pdb.gz'))
def mmcif_1kbu():
return mdt.read(get_data_path('1KBU.cif.bz2'))
def pdb_3ac2_roundtrip(pdb_3ac2):
return mdt.read(pdb_3ac2.write('pdb'), format='pdb')
def protease_cif():
return mdt.read(get_data_path('3aid.cif.bz2'))
def pdb_1hpk():
return mdt.read(get_data_path('1hpk.pdb'))
def nucleic():
# ACTG.pdb contains a molecule generated using mdt.build_dna('ACTG')
mol = mdt.read(get_data_path('ACTG.pdb'))
return mol
def pdb_2jaj():
return mdt.read(get_data_path('2jaj.pdb.gz'))
def pdb3aid():
mol = mdt.read(get_data_path('3aid.pdb.gz'))
return mol
def test_missing_residues_nmr_5b7a():
mol = mdt.read(get_data_path('5b7a.pdb.bz2'))
missingres = mol.metadata.missing_residues
for expected in MISSINGRES_5B7A:
assert missingres[expected[0]][expected[2]] == expected[1]
assert mol.metadata.description == 'STRUCTURES OF HUMAN SUMO'
def pdb_1pyn_roundtrip(pdb_1pyn):
return mdt.read(pdb_1pyn.write('pdb'), format='pdb')
def protease_pdb():
return mdt.read(get_data_path('3aid.pdb.gz'))
def test_single_chain_2p8w():
mol = mdt.read(get_data_path('2p8w.cif.bz2'))
assert mol.num_chains == 3
assert mol.chains['C'].num_residues == 1
assert mol.chains['C'].residues['GNP843'].num_atoms == 32
def bipyridine_xyz():
return mdt.read(get_data_path('bipyridine.xyz'))
def test_read_from_buffer():
s = native_str("2\nmy xyz file\n H 1.0 1.0 1.0\n H 1.0 2.0 1.0\n")
buffer = native_str_buffer(s)
h2 = mdt.read(buffer, format='xyz')
assert h2.num_atoms == 2